Because of the rapid development of multidrug resistance, conventional antibiotics cannot kill pathogenic bacteria efficiently. New antibiotic treatments such as antimicrobial peptides (AMPs) can provide a possible solution to the antibiotic-resistance crisis. However, the identification of AMPs using experimental methods is expensive and time-consuming. Meanwhile, few studies use amino acid compositions (AACs) and physicochemical properties with different sequence lengths against different organisms to predict AMPs. Therefore, the major purpose of this study is to identify AMPs on seven categories of organisms, including amphibians, humans, fish, insects, plants, bacteria, and mammals. According to the one-rule attribute evaluation, the selected features were used to construct the predictive models based on the random forest algorithm. Compared to the accuracies of iAMP-2L (a web-server for identifying AMPs and their functional types), ADAM (a database of AMP), and MLAMP (a multi-label AMP classifier), the proposed method yielded higher than 92% in predicting AMPs on each category. Additionally, the sensitivities of the proposed models in the prediction of AMPs of seven organisms were higher than that of all other tools. Furthermore, several physicochemical properties (charge, hydrophobicity, polarity, polarizability, secondary structure, normalized van der Waals volume, and solvent accessibility) of AMPs were investigated according to their sequence lengths. As a result, the proposed method is a practical means to complement the existing tools in the characterization and identification of AMPs in different organisms.

Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase–substrate phosphorylations with E3 ligase–substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform’s new features—interactive visualization tools and streamlined data downloads—allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.

Alzheimer’s disease (AD) is a neurodegenerative disorder. Though it is not yet curable or reversible, research has shown that clinical intervention or intensive cognitive training at an early stage may effectively delay the progress of the disease. As a result, screening populations with mild cognitive impairment (MCI) or early AD via efficient, effective and low-cost cognitive assessments is important. Currently, a cognitive assessment relies mostly on cognitive tests, such as the Mini-Mental State Examination (MMSE) or the Montreal Cognitive Assessment (MoCA), which must be performed by therapists. Also, cognitive functions can be divided into a variety of dimensions, such as memory, attention, executive function, visual spatial and so on. Executive functions (EF), also known as executive control or cognitive control, refer to a set of skills necessary to perform higher-order cognitive processes, including working memory, planning, attention, cognitive flexibility, and inhibitory control. Along with the fast progress of virtual reality (VR) and artificial intelligence (AI), this study proposes an intelligent assessment method aimed at assessing executive functions. Utilizing machine learning to develop an automatic evidence-based assessment model, behavioral information is acquired through performing executive-function tasks in a VR supermarket. Clinical trials were performed individuals with MCI or early AD and six healthy participants. Statistical analysis showed that 45 out of 46 indices derived from behavioral information were found to differ significantly between individuals with neurocognitive disorder and healthy participants. This analysis indicates these indices may be potential bio-markers. Further, machine-learning methods were applied to build classifiers that differentiate between individuals with MCI or early AD and healthy participants. The accuracy of the classifier is up to 100%, demonstrating the derived features from the VR system were highly related to diagnosis of individuals with MCI or early AD.

Attention-deficit/Hyperactivity disorder(ADHD) is a common neurodevelopmental disorder among children. Traditional assessment methods generally rely on behavioral rating scales (BRS) performed by clinicians, and sometimes parents or teachers. However, BRS assessment is time consuming, and the subjective ratings may lead to bias for the evaluation. Therefore, the major purpose of this study was to develop a Virtual Reality (VR) classroom associated with an intelligent assessment model to assist clinicians for the diagnosis of ADHD. In this study, an immersive VR classroom embedded with sustained and selective attention tasks was developed in which visual, audio, and visual-audio hybrid distractions, were triggered while attention tasks were conducted. A clinical experiment with 37 ADHD and 31 healthy subjects was performed. Data from BRS was compared with VR task performance and analyzed by rank-sum tests and Pearson Correlation. Results showed that 23 features out of total 28 were related to distinguish the ADHD and non-ADHD children. Several features of task performance and neuro-behavioral measurements were also correlated with features of the BRSs. Additionally, the machine learning models incorporating task performance and neuro-behavior were used to classify ADHD and non-ADHD children. The mean accuracy for the repeated cross-validation reached to 83.2%, which demonstrated a great potential for our system to provide more help for clinicians on assessment of ADHD.

Recent studies have demonstrated that the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) could be used to detect superbugs, such as methicillin-resistant Staphylococcus aureus (MRSA). Due to an increasingly clinical need to classify between MRSA and methicillin-sensitive Staphylococcus aureus (MSSA) efficiently and effectively, we were motivated to develop a systematic pipeline based on a large-scale dataset of MS spectra. However, the shifting problem of peaks in MS spectra induced a low effectiveness in the classification between MRSA and MSSA isolates. Unlike previous works emphasizing on specific peaks, this study employs a binning method to cluster MS shifting ions into several representative peaks. A variety of bin sizes were evaluated to coalesce drifted or shifted MS peaks to a well-defined structured data. Then, various machine learning methods were performed to carry out the classification between MRSA and MSSA samples. Totally 4858 MS spectra of unique S. aureus isolates, including 2500 MRSA and 2358 MSSA instances, were collected by Chang Gung Memorial Hospitals, at Linkou and Kaohsiung branches, Taiwan. Based on the evaluation of Pearson correlation coefficients and the strategy of forward feature selection, a total of 200 peaks (with the bin size of 10 Da) were identified as the marker attributes for the construction of predictive models. These selected peaks, such as bins 2410–2419, 2450–2459 and 6590–6599 Da, have indicated remarkable differences between MRSA and MSSA, which were effective in the prediction of MRSA. The independent testing has revealed that the random forest model can provide a promising prediction with the area under the receiver operating characteristic curve (AUC) at 0.8450. When comparing to previous works conducted with hundreds of MS spectra, the proposed scheme demonstrates that incorporating machine learning method with a large-scale dataset of clinical MS spectra may be a feasible means for clinical physicians on the administration of correct antibiotics in shorter turn-around-time, which could reduce mortality, avoid drug resistance and shorten length of stay in hospital in the future.

Background: The use of artificial intelligence (AI) in the medical domain has attracted considerable research interest. Inference applications in the medical domain require energy-efficient AI models. In contrast to other types of data in visual AI, data from medical laboratories usually comprise features with strong signals. Numerous energy optimization techniques have been developed to relieve the burden on the hardware required to deploy a complex learning model. However, the energy efficiency levels of different AI models used for medical applications have not been studied.Objective: The aim of this study was to explore and compare the energy efficiency levels of commonly used machine learning algorithms—logistic regression (LR), k-nearest neighbor, support vector machine, random forest (RF), and extreme gradient boosting (XGB) algorithms, as well as four different variants of neural network (NN) algorithms—when applied to clinical laboratory datasets.Methods: We applied the aforementioned algorithms to two distinct clinical laboratory data sets: a mass spectrometry data set regarding Staphylococcus aureus for predicting methicillin resistance (3338 cases; 268 features) and a urinalysis data set for predicting Trichomonas vaginalis infection (839,164 cases; 9 features). We compared the performance of the nine inference algorithms in terms of accuracy, area under the receiver operating characteristic curve (AUROC), time consumption, and power consumption. The time and power consumption levels were determined using performance counter data from Intel Power Gadget 3.5.Results: The experimental results indicated that the RF and XGB algorithms achieved the two highest AUROC values for both data sets (84.7% and 83.9%, respectively, for the mass spectrometry data set; 91.1% and 91.4%, respectively, for the urinalysis data set). The XGB and LR algorithms exhibited the shortest inference time for both data sets (0.47 milliseconds for both in the mass spectrometry data set; 0.39 and 0.47 milliseconds, respectively, for the urinalysis data set). Compared with the RF algorithm, the XGB and LR algorithms exhibited a 45% and 53%-60% reduction in inference time for the mass spectrometry and urinalysis data sets, respectively. In terms of energy efficiency, the XGB algorithm exhibited the lowest power consumption for the mass spectrometry data set (9.42 Watts) and the LR algorithm exhibited the lowest power consumption for the urinalysis data set (9.98 Watts). Compared with a five-hidden-layer NN, the XGB and LR algorithms achieved 16%-24% and 9%-13% lower power consumption levels for the mass spectrometry and urinalysis data sets, respectively. In all experiments, the XGB algorithm exhibited the best performance in terms of accuracy, run time, and energy efficiency.Conclusions: The XGB algorithm achieved balanced performance levels in terms of AUROC, run time, and energy efficiency for the two clinical laboratory data sets. Considering the energy constraints in real-world scenarios, the XGB algorithm is ideal for medical AI applications.